Alignment visualization and saving

Clicking on the html file (generated by biojs)

• Warning: use the horizontal scrollbar of the window + the right click of the mouse on the alignment to see the left part of the representation.


• To change the aligments colors (“Nucleotide” recommanded for nucleotides):
  
  
  

  



• To annotate the FR and CDR regions, use the biojs.gff file in the same folder than the opened .html file:
  
  
  

  



• Schematic illustration of these regions:
  
  
  

  

  



• Export as picture does not work well as part of the sequence not displayed are not exported (screenshot). Use Jalview, as explained below.

Jalview

In Jalview:

• Drag and drop the .fasta file with the same name as the .html file (in the alignment folder), or use the menu file:
  
  
  

  



• To stain nuc or aa letters:
  • Add colors:
    
    
    

    

  
  
  • Set a threshold to see the differences:
    
    
    

    

  
  
  • A high threshold set all the columns with at least one difference in white:
    
    
    

    

  
  
  • A low threshold set all the different minority events in each column in white:
    
    
    

    



• To add features:
  • Drag and drop a jalview.gff file on the sequence, or use the menu file:
    
    
    

    

  
  
  • To change the feature colors:
    
    
    

    

  
  
  • To reset the features:
    
    
    

    



• To export as .png for instance:
  
  
  

  

Abalign

In Abalign, import a fasta file from the alignment folder and analyze interactively.

Warning: if the align_seq parameter of the nextflow.config file is query, then the vizualization is performed only for the aa sequences that are in phase (i.e., that have identifiable v, d or j regions).